Method dispatch sometimes failsfor lavaan objects

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Method dispatch sometimes failsfor lavaan objects

Ulrich KELLER-3
Hello,

in some R sessions, method dispatch for objects of the (S4) class “lavaan" fail. An example from such a “bad” session:

> library(lavaan)
> HS.model <- ' visual  =~ x1 + x2 + x3
+               textual =~ x4 + x5 + x6
+               speed   =~ x7 + x8 + x9 '
> fit <- cfa(HS.model, data = HolzingerSwineford1939)
> vcov(fit)
Error in UseMethod("vcov") :
  no applicable method for 'vcov' applied to an object of class “lavaan"

But everything _seems_ to be fine:

> selectMethod("vcov", list("lavaan"))
[…]
<environment: namespace:lavaan>

Signatures:
        object  
target  "lavaan"
defined “lavaan"

> pryr::method_from_call(vcov(fit))
[…]
<environment: namespace:lavaan>

Signatures:
        object  
target  "lavaan"
defined “lavaan”

For other calls, R uses the default method instead of the one for lavaan, leading to other errors:

> coef(fit)
Error: $ operator not defined for this S4 class
> traceback()
2: coef.default(fit)
1: coef(fit)

Here too, selectMethod() seems to indicate that everything is fine.

As I mentioned, this happens in “some” R sessions, but I haven’t been able no narrow down what distinguishes “bad” from “good” sessions (where the problem does not occur). I’ve tried starting with a new session with just package lavaan loaded (where it works) and then one by one loading the same packages I have loaded in a bad session, but I can’t reproduce the error in the new session.

Some time ago, somebody posted this problem to the lavaan Google group, but nothing came of it (https://groups.google.com/forum/#!topic/lavaan/LoUemqNhXBM). My hope is that somebody here will have an idea for investigating this problem further.

Thanks a lot in advance,

Uli


Session info from a bad session with almost all objects removed from the workspace and restarted with only lavaan package loaded:

> sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Mojave 10.14.6

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base    

other attached packages:
[1] lavaan_0.6-5

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.3       rstudioapi_0.10  knitr_1.25       magrittr_1.5     tidyselect_0.2.5
 [6] mnormt_1.5-5     pbivnorm_0.6.0   R6_2.4.0         rlang_0.4.1      stringr_1.4.0  
[11] dplyr_0.8.3      globals_0.12.4   tools_3.6.1      parallel_3.6.1   xfun_0.10      
[16] htmltools_0.4.0  assertthat_0.2.1 digest_0.6.22    tibble_2.1.3     crayon_1.3.4    
[21] pryr_0.1.4       purrr_0.3.3      codetools_0.2-16 glue_1.3.1       stringi_1.4.3  
[26] compiler_3.6.1   pillar_1.4.2     stats4_3.6.1     future_1.15.0    listenv_0.7.0  
[31] pkgconfig_2.0.3


Session info from a good session with lots of packages loaded while trying to reproduce the problem:

> sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Mojave 10.14.6

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base    

other attached packages:
 [1] future_1.15.0         rlang_0.4.1           magrittr_1.5          TAM_3.3-10          
 [5] CDM_7.4-19            mvtnorm_1.0-11        semPlot_1.1.2         MplusAutomation_0.7-3
 [9] forcats_0.4.0         stringr_1.4.0         dplyr_0.8.3           purrr_0.3.3          
[13] readr_1.3.1           tidyr_1.0.0           tibble_2.1.3          ggplot2_3.2.1        
[17] tidyverse_1.2.1       psych_1.8.12          semTools_0.5-2        lavaan_0.6-5        

loaded via a namespace (and not attached):
  [1] minqa_1.2.4         colorspace_1.4-1    rjson_0.2.20        htmlTable_1.13.2  
  [5] corpcor_1.6.9       base64enc_0.1-3     rstudioapi_0.10     listenv_0.7.0      
  [9] lubridate_1.7.4     xml2_1.2.2          codetools_0.2-16    splines_3.6.1      
 [13] mnormt_1.5-5        knitr_1.25          glasso_1.11         texreg_1.36.23    
 [17] zeallot_0.1.0       Formula_1.2-3       jsonlite_1.6        nloptr_1.2.1      
 [21] broom_0.5.2         cluster_2.1.0       png_0.1-7           regsem_1.3.9      
 [25] compiler_3.6.1      httr_1.4.1          backports_1.1.5     assertthat_0.2.1  
 [29] Matrix_1.2-17       lazyeval_0.2.2      cli_1.1.0           acepack_1.4.1      
 [33] htmltools_0.4.0     tools_3.6.1         OpenMx_2.14.11      igraph_1.2.4.1    
 [37] coda_0.19-3         gtable_0.3.0        glue_1.3.1          reshape2_1.4.3    
 [41] Rcpp_1.0.3          carData_3.0-2       cellranger_1.1.0    vctrs_0.2.0        
 [45] nlme_3.1-142        lisrelToR_0.1.4     xfun_0.10           globals_0.12.4    
 [49] proto_1.0.0         openxlsx_4.1.3      lme4_1.1-21         rvest_0.3.5        
 [53] ggm_2.3             lifecycle_0.1.0     gtools_3.8.1        XML_3.98-1.20      
 [57] MASS_7.3-51.4       scales_1.0.0        BDgraph_2.61        hms_0.5.2          
 [61] kutils_1.69         parallel_3.6.1      huge_1.3.4          RColorBrewer_1.1-2
 [65] pbapply_1.4-2       gridExtra_2.3       pander_0.6.3        rpart_4.1-15      
 [69] latticeExtra_0.6-28 stringi_1.4.3       sem_3.1-9           checkmate_1.9.4    
 [73] polycor_0.7-10      boot_1.3-23         zip_2.0.4           truncnorm_1.0-8    
 [77] d3Network_0.5.2.1   pkgconfig_2.0.3     Rsolnp_1.16         arm_1.10-1        
 [81] lattice_0.20-38     htmlwidgets_1.5.1   tidyselect_0.2.5    plyr_1.8.4        
 [85] R6_2.4.0            generics_0.0.2      Hmisc_4.3-0         whisker_0.4        
 [89] gsubfn_0.7          pillar_1.4.2        haven_2.2.0         foreign_0.8-72    
 [93] withr_2.1.2         rockchalk_1.8.144   survival_3.1-7      abind_1.4-5        
 [97] nnet_7.3-12         modelr_0.1.5        crayon_1.3.4        fdrtool_1.2.15    
[101] jpeg_0.1-8.1        grid_3.6.1          readxl_1.3.1        qgraph_1.6.3      
[105] data.table_1.12.6   pbivnorm_0.6.0      matrixcalc_1.0-3    digest_0.6.22      
[109] xtable_1.8-4        mi_1.0              stats4_3.6.1        munsell_0.5.0      
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